Abstract
To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three sub-populations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated within and between populations. Based on haplotype kinships a distance measure is proposed which is approximatively linear with the number of generations since fission. The haplotype kinship distances, the respective standard errors and the pedigree-based expected values are presented and are shown to reflect the true population history better than distances based on single-locus kinships. However the marker estimated haplotype kinship reveals variable among segments. This leads to high standard errors of the respective distances. Possible reasons for this phenomenon are discussed and a pedigree-based approach to correct for identical haplotypes which are not identical by descent is proposed.
Highlights
Genetic diversity is required for populations to cope with environmental change and the maintenance of genetic diversity is a primary objective in the management of threatened populations [15]
Excoffier and Slatkin [10] mentioned that the use of markers which are not in Hardy-Weinberg equilibrium (HWE) might lead to biased haplotype frequencies when applying the EMalgorithm
(1) The hypothesis that the haplotype kinship is decreasing with increasing chromosome segment size is clearly confirmed (Figs 3a), 3b), 4a) and 4b))
Summary
Genetic diversity is required for populations to cope with environmental change and the maintenance of genetic diversity is a primary objective in the management of threatened populations [15]. In subdivided populations like livestock species total genetic diversity consists of within and between subpopulation diversity. Between breed diversity is mostly assessed on the basis of genetic distances, for which allele frequencies are used as basic information. In the last years genetic distances estimated from polymorphic microsatellite markers have been the most popular method for the assessment of the phylogenetic structure in animal genetic resources [1, 32]. Genetic distances have statistical and biological properties which are often based on assumptions which do not hold for livestock populations. Without the consideration of those limitations, genetic distance values might become misleading and lose the explanatory power for genetic diversity in livestock breeds. The properties and limitations related to the subject of the study are presented for more detailed discussion a reference to the literature is made [7, 19, 21]
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